Kekulè form parameterized by CHARMM-GUI

User discussions
1

GROMACS version: 2021.1
GROMACS modification: Yes/No
Dear all,
The Kekulè form of my docked ligand parameterized by CHARMM-GUI disappears even if the hybridization of aromatic carbons is sp2.
Can I still move forward with the next steps and create a protein/ligand complex for doing dynamics in Gromacs?

The output picture is: LIG_output

The topologies created by CHARMM-GUI Ligand Reader & Modeler are:

Topologies generated by

  • CHARMM General Force Field (CGenFF) program version 2.4.0

36 1

! “penalty” is the highest penalty score of the associated parameters.
! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

RESI lig 0.000 ! param penalty= 108.000 ; charge penalty= 75.739
GROUP ! CHARGE CH_PENALTY
ATOM C1 CG2R61 -0.323 ! 1.218
ATOM C2 CG2R61 -0.175 ! 0.000
ATOM C3 CG2R61 -0.161 ! 0.000
ATOM C4 CG2R61 -0.085 ! 16.128
ATOM N1 NG2RC0 -0.358 ! 26.590
ATOM C5 CG2RC0 0.284 ! 14.930
ATOM N2 NG2R50 -0.413 ! 20.196
ATOM C6 CG2R51 0.257 ! 35.016
ATOM C7 CG2R51 0.028 ! 75.739
ATOM N3 NG311 -0.629 ! 71.708
ATOM C8 CG331 -0.153 ! 9.334
ATOM H1 HGR61 0.288 ! 0.000
ATOM H2 HGR61 0.124 ! 0.000
ATOM H3 HGR61 0.170 ! 0.000
ATOM H4 HGR62 0.240 ! 0.000
ATOM H5 HGR52 0.266 ! 17.057
ATOM H6 HGPAM1 0.370 ! 5.247
ATOM H7 HGA3 0.090 ! 0.625
ATOM H8 HGA3 0.090 ! 0.625
ATOM H9 HGA3 0.090 ! 0.625

BOND C1 C2
BOND C1 C5
BOND C1 H1
BOND C2 C3
BOND C2 H2
BOND C3 C4
BOND C3 H3
BOND C4 N1
BOND C4 H4
BOND N1 C5
BOND N1 C7
BOND C5 N2
BOND N2 C6
BOND C6 C7
BOND C6 H5
BOND C7 N3
BOND N3 C8
BOND N3 H6
BOND C8 H7
BOND C8 H8
BOND C8 H9

END

2

Molecular mechanics force fields know nothing about hybridization or other quantum concepts. If your molecule distorts, that means some parameters are out of balance. You have very high parameter penalties, so it is not surprising that the molecule has issues. You should not use this topology without further refinement.

3

Dear Justin,
thanks for your reply. I have double-checked the coordinates of the ligand and the error was that when I loaded the trajectories into Pymol for visualization I added the hydrogens with the built-in function. Visual inspection showed me that the planar geometry is maintained.

Schermata 2021-04-02 alle 19.52.24
Schermata 2021-04-02 alle 19.52.241248×1056 119 KB

What if I want to represent my molecule in a Kekule way if I want to present it for a report or publication?

Bests

4

This is a PyMOL issue, not a GROMACS issue. See Valence - PyMOLWiki